Wednesday, July 18, 2012

Own Goal: Evolutionists Explain How Complex Structures Evolved—First They Evolved So Then They Could Evolve

Depending on the environment the roundworm Pristionchus pacificus may develop two very different types of mouth structures. If the developing worm is in a bacteria-rich environment then it develops small teeth and a narrow oral cavity. But if there is a food shortage or overpopulation of worms, then Pristionchus pacificus develops a wide mouth with strong, vicious teeth structures with which to devour other worms. So now those random mutations not only morph species to ever improved designs, they actually design construction mechanisms that switch between alternative morphologies depending on the environment. Truly remarkable.

What may be even more remarkable than evolution’s heroics is how absurdly evolutionists interpret these results. Of course there is no scientific explanation of how those random mutations could have done all this. Nonetheless, bloodied but not bowed evolutionists turn this into yet another triumphant moment. Not only does this remarkable developmental polyphenism show “how frugally evolution works,” but it also facilitates phenotypic evolution. Or in plain English:

Moreover, the existence of alternative body structures is viewed as paving the way for evolution: "In order to change the mouth structure permanently, the genetic control would only have to be decoupled from the environmental dependency," explains Ralf Sommer.

If that still is unclear, the ludicrous message is this: The way evolution constructs such elaborate designs as the worm’s killer oral cavity is first to evolve it as one of two alternatives in a complex developmental program. Then, you get rid of said program, and you’re left only with the killer oral cavity. Presto, just like that evolution evolved a fancy new design. Religion drives science, and it matters.

"switch between alternative morphologies depending on the environments. Truly remarkable."

That is truly remarkable! And as unexpected as that was for it to be found that the environment can control how the information in the genome gets expressed (epigenetics), now, surprisingly, on top of this it is found that 'mental states' can also epigenetically control how the information in the genome gets expressed. i.e. it seems that, very, very, much contrary to the reductive materialistic mindset, we are not merely victims and/or puppets of whatever state our genes happen to be in, but can have some 'epigenetic influence' over our genetic information:

Anxiety May Shorten Your Cell Life - July 12, 2012Excerpt: These studies had the advantage of large data sets involving thousands of participants.If the correlations remain robust in similar studies, it would indicate that mental states and lifestyle choices can produce epigenetic effects on our genes.http://crev.info/2012/07/anxiety-may-shorten-your-cell-life/

Of somewhat related note: The brain has a different, special, type of non-local quantum entanglement on top of the 'normal' type of non-local quantum entanglement that is typically found in the rest of the body, in that different regions of the brain that are separated by large distances, comparatively speaking, can be 'quantumly correlated':

Brain ‘entanglement’ could explain memories - January 2010Excerpt: In both cases, the researchers noticed that the voltage of the electrical signal in groups of neurons separated by up to 10 millimetres sometimes rose and fell with exactly the same rhythm. These patterns of activity, dubbed “coherence potentials”, often started in one set of neurons, only to be mimicked or “cloned” by others milliseconds later. They were also much more complicated than the simple phase-locked oscillations and always matched each other in amplitude as well as in frequency. (Perfect clones) “The precision with which these new sites pick up on the activity of the initiating group is quite astounding – they are perfect clones,” says Plenhttp://www.newscientist.com/article/dn18371-brain-entanglement-could-explain-memories.html

It turns out that non-local quantum information has been confirmed to be in protein structures as well;

Coherent Intrachain energy migration at room temperature - Elisabetta Collini & Gregory Scholes - University of Toronto - Science, 323, (2009), pp. 369-73 Excerpt: The authors conducted an experiment to observe quantum coherence dynamics in relation to energy transfer. The experiment, conducted at room temperature, examined chain conformations, such as those found in the proteins of living cells. Neighbouring molecules along the backbone of a protein chain were seen to have coherent energy transfer. Where this happens quantum decoherence (the underlying tendency to loss of coherence due to interaction with the environment) is able to be resisted, and the evolution of the system remains entangled as a single quantum state. http://www.scimednet.org/quantum-coherence-living-cells-and-protein/

As to establishing that the brain exhibits a different type quantum entanglement than the rest of the body,,

This following video interview of a Harvard Neurosurgeon, who had a deep Near Death Experience (NDE), is very interesting. His NDE was rather unique from typical NDEs in that he had completely lost brain wave function for 7 days while his the rest of his body was on life support. As such he had what can be termed a 'pure consciousness' NDE that was dramatically different from the 'typical' NDEs of going through a tunnel to a higher heavenly dimension, seeing departed relatives, and having a life review.

This gives strong supporting evidence that there are two types of quantum 'linkages' in us. One type of quantum link, found in DNA and proteins on a massive scale, links the 'entire soul' to the body and the other type of quantum link links our mind/consciousness to our brain.

Of note: Here is a 'typical' Near Death Experience in Judeo-Christian cultures:

Near Death Experience – The Tunnel, The Light, The Life Review – videohttp://www.metacafe.com/watch/4200200/

Verses and Music:

Matthew 22:37And he said to him, “You shall love the Lord your God with all your heart and with all your soul and with all your mind.

Luke 23:43Jesus answered him, "I tell you the truth, today you will be with me in paradise."

In the following article, Dr. Hameroff expands on the quantum computation aspect of Rieper, Anders and Vedral (Quantum Entangled DNA) paper:

Is DNA a quantum computer? Stuart Hameroff Excerpt: DNA could function as a quantum computers with superpositions of base pair dipoles acting as qubits. Entanglement among the qubits, necessary in quantum computation is accounted for through quantum coherence in the pi stack where the quantum information is shared,,, http://www.quantumconsciousness.org/dnaquantumcomputer1.htm

Moreover a very high level of information processing is found to be 'missing' upon death:

The Unbearable Wholeness of Beings - Steve TalbottExcerpt: Virtually the same collection of molecules exists in the canine cells during the moments immediately before and after death. But after the fateful transition no one will any longer think of genes as being regulated, nor will anyone refer to normal or proper chromosome functioning. No molecules will be said to guide other molecules to specific targets, and no molecules will be carrying signals, which is just as well because there will be no structures recognizing signals. Code, information, and communication, in their biological sense, will have disappeared from the scientist’s vocabulary.http://www.thenewatlantis.com/publications/the-unbearable-wholeness-of-beings

Permanence (conservation) of quantum information is noted here:

Quantum no-hiding theorem experimentally confirmed for first time - March 2011Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed.http://www.physorg.com/news/2011-03-quantum-no-hiding-theorem-experimentally.html

Quantum no-deleting theoremExcerpt: A stronger version of the no-cloning theorem and the no-deleting theorem provide permanence to quantum information. To create a copy one must import the information from some part of the universe and to delete a state one needs to export it to another part of the universe where it will continue to exist.http://en.wikipedia.org/wiki/Quantum_no-deleting_theorem#Consequence

oleg since you seem to consider yourself an expert on all things to do with evolution and the complexity we find in life, can you please help me with the following:

Do you believe Richard Dawkins exists?Excerpt: DNA is the best information storage mechanism known to man. A single pinhead of DNA contains as much information as could be stored on 2 million two-terabyte hard drives.http://creation.com/does-dawkins-exist

3-D Structure Of Human Genome: Fractal Globule Architecture Packs Two Meters Of DNA Into Each Cell - Oct. 2009Excerpt: the information density in the nucleus is trillions of times higher than on a computer chip -- while avoiding the knots and tangles that might interfere with the cell's ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication.http://www.sciencedaily.com/releases/2009/10/091008142957.htm

Biochemical Turing Machines “Reboot” the Watchmaker Argument - Fazale Rana - July 2012Excerpt: Researchers recognize several advantages to DNA computers.(7) One is the ability to perform a massive number of operations at the same time (in parallel) as opposed to one at a time (serially) as demanded by silicon-based computers. Secondly, DNA has the capacity to store an enormous quantity of information. One gram of DNA can house as much information as nearly 1 trillion CDs. And a third benefit is that DNA computing operates near the theoretical capacity with regard to energy efficiency.http://stevebrownetc.com/2012/07/02/biochemical-turing-machines-%E2%80%9Creboot%E2%80%9D-the-watchmaker-argument/

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome - Oct. 2009Excerpt: At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus.http://www.sciencemag.org/cgi/content/abstract/326/5950/289

The data compression of some stretches of human DNA is estimated to be up to 12 codes thick (12 different ways of DNA transcription) (Trifonov, 1989). (This is well beyond the complexity of any computer code ever written by man). John Sanford - Genetic Entropy - 2005)

Now oleg, with your vastly superior knowledge, I'm sure you should have no problem showing us the exact lab work demonstrating how this level of complexity, that our best computer and software engineers can only dream of imitating, arose by blind undirected neo-Darwinian processes!

What a fascist. Not only do evolutionists suppress dissent in academia, they wish to suppress the free exchange of ideas in an evolutionary critical blog. Truly amazing. And I bet Oleg believes that he believes in free speech. Evolutionary thinking is only for the truly bent mind.

Peter: What a fascist. Not only do evolutionists suppress dissent in academia, they wish to suppress the free exchange of ideas in an evolutionary critical blog.

Absolute rubbish. Nobody here is wishing to "suppress the free exchange of ideas" anywhere, and I could point you at far more sites where evolutionists have been banned from posting than sites where those critical of evolution post. The trouble in my experience is getting IDists to actually show up on pro-evolution blogs.

Moreover, dissent is not notably suppressed in mainstream academia - Behe, for instance, holds an academic post. In stark contrast, academics at religious universities often have to sign up to a specific worldview, and get into serious trouble if they call into question, for example, a literal interpretation of Genesis.

I don't understand what your objection to ba77's posts are? His posts are on topic and link to articles furthering each debate.

Perhaps its your difficulty in addressing the arguments that's the problem?

The objection (mine, anyway) is that, firstly, ba77 rarely makes an actual argument - his links are C&Ps often to videos, and occasionally to academic papers. In the past, when I've followed his links, the videos have turned out to be appalling powerpoint presentations of misinformation about evolution, or anecdotal stories about weird experience, or, when they are to proper scientific evidence, the papers do not support his case (in fact often directly refute it).

When called upon to actually support a statement he makes, he usually bails out (not before calling his interlocutor a liar, again, without providing supporting evidence for the allegation).

In my last exchange, he grudgingly retracted his allegation that I had lied, only to repeat a different one. When I asked him a question that would have allowed him to support his second allegation, he refused to answer.

Typical bait and switch. You demonstrate fascist behaviour and then make a ridiculous admission to distract from the subject. It must come naturally to evolutionists as a defense mechanism to deny reality.

Elizabeth Liddle: "When called upon to actually support a statement he makes, [bornagain77] usually bails out (not before calling his interlocutor a liar, again, without providing supporting evidence for the allegation). In my last exchange, he grudgingly retracted his allegation that I had lied, only to repeat a different one. When I asked him a question that would have allowed him to support his second allegation, he refused to answer."

That is par for the course. Bornagain77 has continually demonstrated that he doesn't even know what 'lying' means. like Cornelius in a recent article, If someone states something that he believes to be factually incorrect, it automatically qualifies as 'lying'. Yet, he doesn't consider 'an intentional attempt to deceive' to be a lie in all cases.

I'd suggest that Cornelius considers it lying because of the particular conception of human knowledge he holds, which includes the idea that we all know God exists and that knowledge is justified only through authoritative sources. In the case of the knowledge of how to build biological adaptations, as found in the genome, that authoritative source was Yahweh. We supposedly know this is true, but reject it, so we're either lying to others or to ourselves.

I'd also suggest that these assumptions are the basis for his clams that evolutionary processes are random, that evolutionary theory unlikely and absurd, etc. Specifically, he thinks that evolutionary processes could not create knowledge because they not an authoritative agent.

Of course, Cornelius could simply deny that holds this particular conception of human knowledge, or that we supposedly know that God exists.

However, Given that the above are core fundamentalist assumptions based on scripture, it's reasonable to assume that Cornelius actually does hold these views as a confessing Christian. Nor does it seem that he can actually publicly deny holding these views as he is employed by fundamentalist Christian college.

So, his best option is to refuse to even acknowledge any questions designed to clarify his position on these issues, even when posed to him directly, over and over again.

"it is a mechanism which has been directly observed in both the lab and field."

'observed in the lab' and found to fail!

Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) - October 2010Excerpt: "Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, "This research really upends the dominant paradigm about how species evolve," said ecology and evolutionary biology professor Anthony Long, the primary investigator.http://www.arn.org/blogs/index.php/literature/2010/10/07/experimental_evolution_in_fruit_flies

The Fate of Darwinism: Evolution After the Modern Synthesis - David J. Depew and Bruce H. Weber - 2011Excerpt: We trace the history of the Modern Evolutionary Synthesis, and of genetic Darwinism generally, with a view to showing why, even in its current versions, it can no longer serve as a general framework for evolutionary theory. The main reason is empirical. Genetical Darwinism cannot accommodate the role of development (and of genes in development) in many evolutionary processes.,,,http://www.springerlink.com/content/845x02v03g3t7002/

Waiting Longer for Two Mutations - Michael J. BeheExcerpt: Citing malaria literature sources (White 2004) I had noted that the de novo appearance of chloroquine resistance in Plasmodium falciparum was an event of probability of 1 in 10^20. I then wrote that 'for humans to achieve a mutation like this by chance, we would have to wait 100 million times 10 million years' (1 quadrillion years)(Behe 2007) (because that is the extrapolated time that it would take to produce 10^20 humans). Durrett and Schmidt (2008, p. 1507) retort that my number ‘is 5 million times larger than the calculation we have just given’ using their model (which nonetheless "using their model" gives a prohibitively long waiting time of 216 million years). Their criticism compares apples to oranges. My figure of 10^20 is an empirical statistic from the literature; it is not, as their calculation is, a theoretical estimate from a population genetics model.http://www.discovery.org/a/9461

More from Ann Gauger on why humans didn’t happen the way Darwin said - July 2012Excerpt: Each of these new features probably required multiple mutations. Getting a feature that requires six neutral mutations is the limit of what bacteria can produce. For primates (e.g., monkeys, apes and humans) the limit is much more severe. Because of much smaller effective population sizes (an estimated ten thousand for humans instead of a billion for bacteria) and longer generation times (fifteen to twenty years per generation for humans vs. a thousand generations per year for bacteria), it would take a very long time for even a single beneficial mutation to appear and become fixed in a human population.You don’t have to take my word for it. In 2007, Durrett and Schmidt estimated in the journal Genetics that for a single mutation to occur in a nucleotide-binding site and be fixed in a primate lineage would require a waiting time of six million years. The same authors later estimated it would take 216 million years for the binding site to acquire two mutations, if the first mutation was neutral in its effect.Facing FactsBut six million years is the entire time allotted for the transition from our last common ancestor with chimps to us according to the standard evolutionary timescale. Two hundred and sixteen million years takes us back to the Triassic, when the very first mammals appeared. One or two mutations simply aren’t sufficient to produce the necessary changes— sixteen anatomical features—in the time available. At most, a new binding site might affect the regulation of one or two genes.http://www.uncommondescent.com/intelligent-design/more-from-ann-gauger-on-why-humans-didnt-happen-the-way-darwin-said/

Your problem is that you get all your scientific information from ID sites. I cannot state it clearly enough - these sites exist for the sole purpose of telling you that ToE is wrong and ID is right. That is their raison d'etre. It's not EXACTLY that they lie to you (though that can and does happen), but there's a Hell of a lot of misrepresentation you can do before you cross the threshhold into a direct lie.

Try linking to an actual scientific study - not one that is being viewed through the crazy-tinted lenses of your ID-site of choice, and explain in your own words exactly what you think that paper shows.

CH: [quotes article:] Moreover, the existence of alternative body structures is viewed as paving the way for evolution: "In order to change the mouth structure permanently, the genetic control would only have to be decoupled from the environmental dependency," explains Ralf Sommer.

CH: If that still is unclear, the ludicrous message is this: The way evolution constructs such elaborate designs as the worm’s killer oral cavity is first to evolve it as one of two alternatives in a complex developmental program.

It is obviously unclear to you, Cornelius. Let me try to explain:

First of all a regulatory sequence appears that effects the expression of genes during development, and is differential activated by environmental signals. Clearly any variant of this sequence that tends to produce an advantageous mouth in environment A in response to signals from environment A and an advantageous mouth in environment B in response to signals from environment B is going to confer enhanced reproductive success, over variants that do it the other way round, or do only one of the two.

So we have powerful selective pressure for variants in which the environmental signals tend to result in a phenotype that does well in that environment.

But such system, once evolved (by natural selection) will mean that should Environment A become the dominant environment, any variant of the sequence that produces a phenotype that reproduces well in Environment A will be conserved, whereas variants produce a phenotype that reproduces well in Environment B in response to Environment B signals, will not be. Thus the relationship between environmental signal and phenotype will be decoupled and the phenotype associated with Environment A will become permanent.

You could demonstrate this for yourself very easily, Cornelius, in a simple model. Far from being "ludicrous" it is extremely straightforward.

Thus the relationship between environmental signal and phenotype will be decoupled and the phenotype associated with Environment A will become permanent.

So evolution is driven by the environment, except in those cases when it isn't driven by the environment.

You've faithfully followed the paradigm explanation found at Wikipedia, but this is simply another "epicycle" that must be amended to Darwinian theory to make it work. As in the Ptolemaic view, maybe the view--the hypothesis--is simply wrong.

BTW, how do we know that Biston Bistulleria and the Galapagos finches aren't environmentally driven developmental processes?

IOW, the "classic" cases of Darwinian evolution may be no more than environmental triggering of what is already present in the genome. If that's the case, then they are no examples of neo-Darwinism at work in the least.

You need genes that make mouth A sometimes and mouth B sometimes. And you need genes that control which genes are turned on. Then you have to get lucky so that the right genes turn on the right genes to make the right mouth at the right time. If it evolved genes that made a type A mouth in response to a type B environment, that wouldn't work.

Well, you need genes that express the proteins involved. However, it's likely that the same genes are involved in both mouth types.

And you need genes that control which genes are turned on.

Exactly. That's the really important part. What makes multicellular organisms take the morphology they do is not so much which protein-coding genes they have, but which genes that modulate the expression of the protein-coding genes during development. So exactly the same genes might be involved (and probably are) in making Mouth A and Mouth B, and exactly the same regulatory genes, but those regulatory genes activity is a function of environmental signals.

Then you have to get lucky so that the right genes turn on the right genes to make the right mouth at the right time.

Sure - but the point is that the ones that don't get lucky don't have as many offspring. The ones that get variants of the regulatory sequence that tends to produce Mouth A in response to environmental signal A and a more B like mouth in response to environmental signal B will tend to leave more offspring.

So sure, some organisms have to get lucky. But the whole point of Darwin's insight is that it doesn't matter which, because, the "lucky" organisms" will leave the most children, and so their genomes will preferentially dominate the population.

If it evolved genes that made a type A mouth in response to a type B environment, that wouldn't work.

Well, watch that word "evolve" - populations evolve, not individual organisms. An organism that finds itself with variant genes that make a type A mouth in response to a type B environment "won't work", indeed, and won't pass those variants on to many offspring.

Bu there are so many parts that have to be in place for this to work. You need the genes that code for the A or B mouth. You need the gene that turns that gene off and on. This means that the organism has to get really, really lucky. And how many mutations does it take to make this whole system. Don't we need to know that?

Let's say that Gene P expresses proteins required for tail length, and Gene R is a regulatory gene that turns Gene A on.

In Organism A, Gene R is a variant that is turned on for about 2 weeks in early development (Allele 1). In Organism B, Gene R is turned on for slightly longer (Allele 2).

This means that Organism B will have a longer tail than Organisms A. If the Environment J is one in which a longer tail is an advantage, Allele 2 of Gene R will become more prevalent in the population.

Now, let's say that the environment fluctuates - sometimes Environment J predominates, sometimes Environment K, in which a shorter tail is an advantage.

Now, both alleles of Gene R will tend to be conserved, because sometimes Allele 1 will be beneficial, and sometimes Allele 2.

Now, another few variants of Gene R comes along - in thes variant, the activity of Gene R is not only affected by cell signalling from neighouring developing tissues but also by signals from environment. Some of these variants are turned on by Environment J and some by environment K.

Clearly variants that are turned on by Environment K will by unsuccessful, because the very environment in which a shorter tail is advantageous is the very environment that lengthens the tail. However, the variant that is turned on by Environment J will be very advantageous, because in those organisms, where Environment J is present, the tail will grow longer, but where Environment K is present, it will tend to be shorter.

There is therefore selective pressure for this particular variant, because, regardless of which Environment is present during its development, it will tend to thrive, and its offspring, even if they are born during a different Environment, will also be kitted out with the best kind of tail.

So sure, the first organism with the neat variant is "lucky" - and the first organisms with the bad variants are "unlucky" - but that's irrelevant. For evolution to occur, only one organism needs to "get lucky" - because it's "luck" consists of lots of offspring bearing the same "lucky" variant - and that isn't "luck" at all, it's simple heredity.

The worm's mouth is different than a tail that can come in two lengths. There isn't just a difference in size. The big mouth kind has those scary teeth. Can it really be controlled by just one gene that is activated for shorter or longer periods?

Probably by several genes, but the important point to bear in mind is that we are talking about a system in which the expression of the genes is modulated by the expression of other genes.

To take a silly example - the genes that result in making skin are not independent of the genes that make our bones, so we do not find our selves with big bones and not enough skin to cover them. The expression of skin genes is affected by the expression of bone genes.

This is why, unlike human engineering designs, biological "designs" are so robust to variance. You don't have to luckily inherit a set of genes that make bits of all the right size. That means that a regulatory gene that "codes for" long legs, doesn't have to have a separate signal for every gene involved in making legs. Rather, it sends a single signal that initiates a cascade of signals that result in a viable leg, whatever length that leg is.

Now, you can marvel at this system in itself - a robust system in which most combinations of variants of many genes still results in a viable organism.

But given that that is the way it works, we don't have to posit any remarkable "luck" that a regulatory gene evolves that is responsive to environmental cues, which then produce a cascade of signals that results in a viable mouth equipped with commensurate teeth.

And remember - mutation isn't "random" in the sense that a lot of people understand the word. Mutations have a probability distribution with a sharp peak over "viable". Most mutations work. You have to be unlucky to get a duff one. And even if you do, the population isn't any worse off, because your duff mutation won't be copied into the population.

"To take a silly example - the genes that result in making skin are not independent of the genes that make our bones, so we do not find our selves with big bones and not enough skin to cover them. The expression of skin genes is affected by the expression of bone genes."

This is probably the question biology still didn`t answer. Because it is not only regulation/coordination of expression of genes. To that you need differential activation of genes according to the position of the cell in the body.

"Mutations have a probability distribution with a sharp peak over "viable". Most mutations work."

That is new. Let me refrase to be sure I understood.The errors in DNA transcritions are more probable when it leads to viable mutations than when it leds to get a duff.I wonder to know the biochemical mechanism for that.

Blas: Because it is not only regulation/coordination of expression of genes. To that you need differential activation of genes according to the position of the cell in the body.

Well, but that is all part of regulation. Gene expression is governed by chemical inputs. Some of these are from neighbouring cells; some are from the whole organism; some are from the external environment; some impact on development; some govern how the cell responds to the organisms needs.

The point is that once you have gene expression modulated by anything else, then you have the potential for the evolution of responsive organisms.

That is new. Let me refrase to be sure I understood.The errors in DNA transcritions are more probable when it leads to viable mutations than when it leds to get a duff.I wonder to know the biochemical mechanism for that.

Well, firstly, don't think of them as "errors" - just variants. After all, many mutations are the result of recombination, which isn't exactly an "error".

Secondly, variants are, by definition, variants on something that works. We know that similar genomes produce similar phenotypes. Therefore the chances of getting a variant that is radically different from its (viable) parent is far smaller than one that is very similar (and similarly viable).

A lot of the fallacious probability arguments advanced in favour of ID seem to be based on the (implicit - usually not explicit, as it is clearly false) assumption that novel sequences are as though drawn nucleotide by nucleotide from a bag of nucleaotides. They obviously are not. Novel sequences are generally very close to parental sequences, which, by definition, work.

"Some of these are from neighbouring cells; some are from the whole organism; some are from the external environment; some impact on development; some govern how the cell responds to the organisms needs.

The point is that once you have gene expression modulated by anything else, then you have the potential for the evolution of responsive organisms."

This seems an oversimplifications, one of the many that evolutionists do. To make the shape of the nose eaxh cell of the cartilage of the nose of my son should know how many times to divide. In order to build the nose shape of my father in my son the DNA needs more than protein genes and expression modulators activated by hormons or adjacent cells (unless also them “knows” where they are and what todo.

“Well, firstly, don't think of them as "errors" - just variants.”

The concept of error comes from the idea that all the machinery of DNA replications tries to make exactly duplicates, Variants is a concept that opens the door to think that this machanisms allows “deliberatly” modificatins in the duplicates. Are you claiming that?

“ After all, many mutations are the result of recombination, which isn't exactly an "error".”

A perfect recombination do not led to mutations unless you are referring to the recombination programmed to produce antibodies. What tipe of recombinations are you referring. How many of the total mutations are cused by recombinations?

“Secondly, variants are, by definition, variants on something that works. We know that similar genomes produce similar phenotypes. Therefore the chances of getting a variant that is radically different from its (viable) parent is far smaller than one that is very similar (and similarly viable).”

Sorry that means most mutations survives, not most mutations works.

“A lot of the fallacious probability arguments advanced in favour of ID seem to be based on the (implicit - usually not explicit, as it is clearly false) assumption that novel sequences are as though drawn nucleotide by nucleotide from a bag of nucleaotides. They obviously are not. Novel sequences are generally very close to parental sequences, which, by definition, work.”

I think you do not understand the ID point, but I`m not going to defend them.

Well, let's say you have a population in a habitat which Environment A and Environment B fluctuate rapidly (for example, as in the Galapagos, where El Nino is a frequent, but not annual, event) - such a habitat will tend to favour organisms in which the environment itself affects the development of a successful phenotype. However, if things change, and Environment A predominates, any variant that tends to result in phenotype A will be conserved, including those variants where phenotype A is not dependent on signals from Environment A. Conversely, any variant that can result in Phenotype B will not be conserved, because there is no longer any selective pressure for this capacity.

Thus the environmental coupling of Environment A with Phenotype A may be broken.

CH: Of course there is no scientific explanation of how those random mutations could have done all this.

Except, you've been provided criteria for demarcation along with a explanation that meets said demarcation. You have yet to provide a detailed criticism of either.

What we get in posts such as this are expressions of incredulity, rather than a detailed argument.

Again, I'd suggest you think evolutionary theory is absurd because you hold a pre-elightenment, authoritative conception of human knowledge. Specifically, the idea that the knowledge of how to build biological adaptations came non-authorative source is absurd to you. Nor do you recognize this conception as an idea that would be subject to criticism.

Apparently, you think your conception is so "obviously" right that you cannot recognize it as an idea that would be subject to criticism and think there is no need to present an actual argument.

Why don't you start out by explaining how knowledge is created, then point out how evolutionary processes do not fit that explanation. Please be specific.

Otherwise, this is more of the same hand waving we see here on a regular basis.

BA77, if you had boxes that were labeled "data contradictory to evolution" and "evidence for intelligent design", these evolutionists here are already against whatever is in the box. They do not care about evidence, they have their argument based on their metaphysical view of the world, they have bird beaks and guppies and a fossil field a mile deep and the size of the earth that they force fit to whatever interpretation that suits them at the moment.

There's an interesting piece over at Discovery that quotes Venter,

"All living cells that we know of on this planet are 'DNA software'-driven biological machines comprised of hundreds of thousands of protein robots, coded for by the DNA, that carry out precise functions," said Venter. "We are now using computer software to DESIGN new DNA software."

http://www.evolutionnews.org/2012/07/software_machin062211.html

Evolutionists are hypocritical here. If their mechanisms could be shown in realtime to have the effect that Venter's design procedures have they would be celebrating in the streets and pontificating from the roofs tops how stupid skeptics are. The power that design has been shown to produce is what evolutionists so badly want their mechanisms to show.

Neal: They do not care about evidence, they have their argument based on their metaphysical view of the world, they have bird beaks and guppies and a fossil field a mile deep and the size of the earth that they force fit to whatever interpretation that suits them at the moment.

This is simply not true, Neal. I'm not sure if you really believe it, or are simply repeating it in the hope that it is true, but it is not true.

"Evolutionists" include many scientists (myself for instance) and scientists care deeply about evidence. It's our livelihood.

Neal Tedford: "if you had boxes that were labeled "data contradictory to evolution" and "evidence for intelligent design", these evolutionists here are already against whatever is in the box. They do not care about evidence,"

Neal, if you had those two boxes, I would do anything to look inside them. I want to know if what I believe is true, and I believe the best way to accomplish that goal is by evaluating evidence.

As Elizabeth asked, do you actually believe that we don't care about evidence, or is that just what you hope? Does repeating that to yourself help you sleep at night?

The only reason I can think of as to why someone wouldn't be interested in evidence is if they believed they already possessed an infallible source of knowledge. Say, and old divinely inspired book or something.

Neal "these evolutionists here are already against whatever is in the box"

True, design is not even a option in their view! Moreover by force fitting everything into a neo-Darwinian worldview, no matter what the evidence says to the contrary, evolutionists end up hampering true scientific progress.

In fact, as to the somewhat minor extent evolutionary reasoning has influenced medical diagnostics, it has led to much ‘medical malpractice’ in the past:

Evolution's "vestigial organ" argument debunked Excerpt: "The appendix, like the once 'vestigial' tonsils and adenoids, is a lymphoid organ (part of the body's immune system) which makes antibodies against infections in the digestive system. Believing it to be a useless evolutionary 'left over,' many surgeons once removed even the healthy appendix whenever they were in the abdominal cavity. Today, removal of a healthy appendix under most circumstances would be considered medical malpractice" (David Menton, Ph.D., "The Human Tail, and Other Tales of Evolution," St. Louis MetroVoice , January 1994, Vol. 4, No. 1). "Doctors once thought tonsils were simply useless evolutionary leftovers and took them out thinking that it could do no harm. Today there is considerable evidence that there are more troubles in the upper respiratory tract after tonsil removal than before, and doctors generally agree that simple enlargement of tonsils is hardly an indication for surgery" (J.D. Ratcliff, Your Body and How it Works, 1975, p. 137). The tailbone, properly known as the coccyx, is another supposed example of a vestigial structure that has been found to have a valuable function—especially regarding the ability to sit comfortably. Many people who have had this bone removed have great difficulty sitting. http://www.ucg.org/science/god-science-and-bible-evolutions-vestigial-organ-argument-debunked/

Further notes on Neo-Darwinism’s negative effect on science and societyhttps://docs.google.com/document/d/1lwdaq8r5K0JbzNtTU4-UqB3t-giK2-hUlsFrNDiJ7Ok/edit

As to suppressing dissenting viewpoints from Darwinism in academia, well, one doesn't have to look far to find evidence:

On the Fundamental Difference Between Darwin-Inspired and Intelligent Design-Inspired Lawsuits - September 2011 Excerpt: Darwin lobby litigation: In every Darwin-inspired case listed above, the Darwin lobby sought to shut down free speech, stopping people from talking about non-evolutionary views, and seeking to restrict freedom of intellectual inquiry. http://www.evolutionnews.org/2011/09/on_the_fundamental_difference_050451.html

"Evolution is the only 'scientific theory' that needs laws to protect it!" Author Unknown

Evolutionary theory contributes little to experimental biologyExcerpt: "Certainly, my own research with antibiotics during World War II received no guidance from insights provided by Darwinian evolution. Nor did Alexander Fleming's discovery of bacterial inhibition by penicillin. I recently asked more than 70 eminent researchers if they would have done their work differently if they had thought Darwin's theory was wrong. The responses were all the same: No.

I also examined the outstanding biodiscoveries of the past century: the discovery of the double helix; the characterization of the ribosome; the mapping of genomes; research on medications and drug reactions; improvements in food production and sanitation; the development of new surgeries; and others. I even queried biologists working in areas where one would expect the Darwinian paradigm to have most benefited research, such as the emergence of resistance to antibiotics and pesticides. Here, as elsewhere, I found that Darwin's theory had provided no discernible guidance, but was brought in, after the breakthroughs, as an interesting narrative gloss.,,,

Darwinian evolution – whatever its other virtues – does not provide a fruitful heuristic in experimental biology. This becomes especially clear when we compare it with a heuristic framework such as the atomic model, which opens up structural chemistry and leads to advances in the synthesis of a multitude of new molecules of practical benefit. None of this demonstrates that Darwinism is false. It does, however, mean that the claim that it is the cornerstone of modern experimental biology will be met with quiet skepticism from a growing number of scientists in fields where theories actually do serve as cornerstones for tangible breakthroughs. Philip S. Skell - (the late) Professor at Pennsylvania State University. http://www.discovery.org/a/2816

Podcasts and Article of Dr. Skellhttp://www.evolutionnews.org/2010/11/giving_thanks_for_dr_philip_sk040981.html

It is in mine! Who are this mysterious 'they' you are referring to? You keep saying "they believe this, they believe that," and we keep correcting you that: "No, we don't believe this, we don't believe that." I don't rule out design from the get-go. We could have been designed by a god. We could have been designed by other natural beings. We could have evolved with divine intervention. We could have evolved by natural processes. I don't rule out any of those options a-priori. I just think the evidence favors the last one.

Design is an option for me. If you can show me how you'd demonstrate design, I'm be all ears. Unverifiable design, however, is not something I'd consider, not because it's design, but because it's unverifiable. Unverifiable hypotheses are useless whether they posit design or not.

...And BA, since I've been absent from the site for a few months, I don't believe you ever gave your definition of 'lying' from a previous conversation we were having. I was reminded of this when Cornelius said in a previous article:

CH: "Evolutionists lie without even realizing it." - "The Difference between Science and Evolution"

I found this odd, because for the second time in a few months, here is a Christian being utterly confused by what a "lie" is. Once simply can not lie without realizing it; a lie is an attempt to deceive. If one says something that they believe to be true, and it is not, then they are merely incorrect; they are not lying.

Perhaps you or Cornelius can clear this up by providing your definition of 'lying'.

Seriously? We are not living in the steam train era. As I posted earlier DNA design is a recognized field of research that has been granted many patents by the US Patent Office. Do you not see this? What is Venter doing, making chicken dumplings?

Seriously? We are not living in the steam train era. As I posted earlier DNA design is a recognized field of research that has been granted many patents by the US Patent Office. Do you not see this? What is Venter doing, making chicken dumplings?

Neal Tedford: "Seriously? We are not living in the steam train era. As I posted earlier DNA design is a recognized field of research that has been granted many patents by the US Patent Office. Do you not see this? What is Venter doing, making chicken dumplings?"

Neal, surely even someone as dense as you can see the obvious fallaciousness of that line of reasoning. "Man can design DNA, therefore all DNA is designed." Well, man can design rocks. Does that mean all rocks are designed? Man can design canyons, does that mean the Grand Canyon is designed? An artist can paint a sunset. Does that mean all sunsets are manmade? Good grief. How have you made it this far?

Neal Tedford: "You wanted someone to demonstrate design. I pointed you to Venter. We have real life examples of the power of intentional Dna design. It is a reasonable option for someone who is not closed minded."

I can just imagine you as a lawyer:

"Yes your honor, I can demonstrate murder. The defendant, John Smith, claims that he was conducting an interview on live television in another state at the time of the murder that he is accused of, but I submit to you exhibit A: Video evidence of Jane Doe committing murder on August 5th, 1982. A murder. Committed. On tape. Therefore, the defendant obviously guilty to anyone who is not close-minded, and I rest my case."

As Thorton said, that's some weapons-grade stupid. What I find fascinating about you Neal, is both your complete lack of self-awareness, and the fact that you will continually defend anything you've previously said, no matter how clearly it is pointed out to you that it either wrong or mind bogglingly stupid.

This is another case of that. I just feel patronizing pointing out that you can't demonstrate that DNA was designed just because we can modify it and come up with our own implementations. It's just like saying that since we can quarry rock, the Grand Canyon must have been quarried. I really don't understand how you can't see how absurd that argument is.

Providing an example of design is not the same thing as demonstrating that something else was designed.

And regarding Venter's design; You not only have the ability to converse with the designer and ask him any question you want, he provided verifiable documentation about how the design was implemented, when the design was implemented, and what methods and tools were used. And as icing on the cake, he can even explain not only why he implemented the design at all, but why he implemented it in the specific way that he did. Does ID have anything remotely like that? If so, I'm all ears.

Derrick said, "providing an example of design is not the same thing as demonstrating that something else was designed"

Venters work is not about painting sunsets and designing rocks. His company is designing new DNA, changing allele frequencies by intentional manipulation of DNA.

Isn't this what evolutionists beg us to have faith in when they tell us about natural selection? Evolutionists observe change in bird beaks and extrapolate the same mechanisms of evolution to the evolution of T-Rex and every life form in the history of the earth. Why, specifically, did T-Rex evolve the way he did? Evolutionists can't give a detailed mutation history of the ancestry of T-Rex or any other animal. We hear a lot about convergence from evolutionists. How specific is that? You have two standards here.

What Venter and many others have shown is that DNA can be manipulated by design that has nothing to do with evolution. Tremendous biological change (not talking about rocks and paintings) can be quickly generated via the tools and procedures of intentional design.

Your canyon analogy is poor because DNA is not rock and possesses information that is encoded and translated and used to build robots. But let's go with it for a minute. Man is capable of quarrying the Grand Canyon (lots of work and time, but possible) and so is water and erosion. The capability of both has been observed and understood. I don't see evolution as having been observed to do much (bird beaks, peppered moths, E Coli). It is like you're speculating earth worm ability to create grand canyon results. It's superstition.

You seem to be hung on the "why" of a designer and unable to disconnect that from the properties or potential of design. Seriously you must know "why" something is designed before accepting that it's designed? Double standard. You always go toward the metaphysical. That's what its all about for you. God wouldn't have done it this way. What's really eating you... The earth was not formed in 144 hours and therefore I'm not seeking Christ anymore?

Evolutionists have no metric or standard for determining design. If something in life was designed, evolutionists have no way of determining it. Everything is automatically the result of evolution. Why? Because of bird beaks, peppered moths and such like. You must know why the designer did such and such. But, regarding evolution, you can bask in generalizations and hand waving stories about natural selection and convergence, etc.

None of us were around to see the history of life on planet earth, so we all must make inferences. Design can move the rock and it can move the DNA. It is a reasonable inference. While erosion can move the rock, we haven't observed the mechanisms of evolution doing too much with DNA.

Who would win a contest in producing the most change in DNA in E Coli... Venter software design or Lenski's evolution? The future is ID.

Derrick said, "providing an example of design is not the same thing as demonstrating that something else was designed"

Design can move the rock and it can move the DNA. It is a reasonable inference. While erosion can move the rock, we haven't observed the mechanisms of evolution doing too much with DNA

Tedford, that's not just weapons grade stupid, it's WMD stupid.

You're claiming that since someone can carve wood to produce a sculpture that the original tree must be designed.

As already pointed out, you are probably the most completely self-unaware dolt on this site. Natural processes that change and create new genetic sequences have been empirically observed for over half a century.

Your willful ignorance about things you've been corrected on a dozen times is just staggering.

Lack of Signal Is Not a Lack of Information - July 18, 2012Excerpt: Putting it all together:The NFL (No Free Lunch) Theorems show that evolution is stuck with a blind search. Information lights the path out of blind search; the more information, the brighter the light.Complex specified information (CSI) exceeds the UPB, so in the evolutionary context a blind search is not an option.Our uniform experience with CSI is that it always has an intelligent cause.Evolution is disconfirmed by negative arguments (NFL theorems and the UPB). Intelligent design is confirmed by positive arguments (uniform experience and inference to the best explanation).http://www.evolutionnews.org/2012/07/lack_of_signal062231.html

Origins - Statistical Impossibility of Evolution with Ralph Muncaster - video (Mr. Muncaster holds a BS in engineering and an MBA from the University of Colorado. A former atheist and hardcore Bible skeptic, Ralph spent 15 years conducting research to dispute the Bible.)http://www.youtube.com/watch?v=DXIAbd8pYQM

That ENV post begins with a seriously stupid statement: "In his book No Free Lunch, Bill Dembski demonstrated that no evolutionary algorithm is superior to a random search."

First, the no-free-lunch theorems were the work of Wolpert and MacReady, not Dembski. Second, they state, basically, that any search does as well as any other search (including a random one) if you average their performance over all possible fitness landscapes. Well, guess what? The evolutionary fitness landscape is not averaged, it stays fixed over the relevant time scale. That means the NFL theorems do not apply to this case. As a result, evolution can do better than a random walk through the landscape.

Do you have a demonstrated example of undirected processes generating 500 bits or above of novel functional information?

“The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain - Michael Behe - December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.(that is a net 'fitness gain' within a 'stressed' environment i.e. remove the stress from the environment and the parent strain is always more 'fit') http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/

Michael Behe talks about the preceding paper on this podcast:

Michael Behe: Challenging Darwin, One Peer-Reviewed Paper at a Time - December 2010http://intelligentdesign.podomatic.com/player/web/2010-12-23T11_53_46-08_00

More from Ann Gauger on why humans didn’t happen the way Darwin said - July 2012Excerpt: Each of these new features probably required multiple mutations. Getting a feature that requires six neutral mutations is the limit of what bacteria can produce. For primates (e.g., monkeys, apes and humans) the limit is much more severe. Because of much smaller effective population sizes (an estimated ten thousand for humans instead of a billion for bacteria) and longer generation times (fifteen to twenty years per generation for humans vs. a thousand generations per year for bacteria), it would take a very long time for even a single beneficial mutation to appear and become fixed in a human population.You don’t have to take my word for it. In 2007, Durrett and Schmidt estimated in the journal Genetics that for a single mutation to occur in a nucleotide-binding site and be fixed in a primate lineage would require a waiting time of six million years. The same authors later estimated it would take 216 million years for the binding site to acquire two mutations, if the first mutation was neutral in its effect.Facing FactsBut six million years is the entire time allotted for the transition from our last common ancestor with chimps to us according to the standard evolutionary timescale. Two hundred and sixteen million years takes us back to the Triassic, when the very first mammals appeared. One or two mutations simply aren’t sufficient to produce the necessary changes— sixteen anatomical features—in the time available. At most, a new binding site might affect the regulation of one or two genes.http://www.uncommondescent.com/intelligent-design/more-from-ann-gauger-on-why-humans-didnt-happen-the-way-darwin-said/

Neal Tedford Venters work is not about painting sunsets and designing rocks. His company is designing new DNA, changing allele frequencies by intentional manipulation of DNA. Isn't this what evolutionists beg us to have faith in when they tell us about natural selection?."

What in the blue blazes are you talking about? What evolutionist has ever said that natural selection has anything to do with intentional manipulation of DNA? What evolutionist has ever advocating having 'faith' in anything? Most of us think 'faith' is a useless tool, at best. I may be giving you and that sentence waaay too much credit in assuming that it's even decipherable in the first place. You constantly surprise me by continually topping the amount of incoherence you can cram into a sentence.

Neal Tedford: What Venter and many others have shown is that DNA can be manipulated by design that has nothing to do with evolution.

What position do you imagine you're arguing against? Of course DNA can be manipulated by design. Who has ever said it can't? Of course human manipulation of DNA isn't an example of evolution. Who has ever said it was? How does it relate to the subject at all? Can you really not see the idiocy in saying "X can be modified by humans, therefore all cases of X are designed?"

Neal Tedford: Man is capable of quarrying the Grand Canyon (lots of work and time, but possible) and so is water and erosion. The capability of both has been observed and understood.

Hold on there a sec.No one has ever observed water carve out a significant amount of rock. We've seen what one might call 'micro-erosion' - water eroding small amounts of rock - measured in centimeters per human lifetime, but no one has observed 'macro-erosion'. It is an inference. And if no has ever observed it happening, how can you say that it even happened? By extrapolating small amounts of erosion over long periods of time? But you've claimed many times that that type of extrapolation is absurd.

Neal Tedrofrd: "I don't see evolution as having been observed to do much (bird beaks, peppered moths, E Coli)."

Well, I don't see erosion has been observed to do much. (removing centimeters of rock, causing small cracks, causing rocks to roll downhill) Those superstitious geologists extrapolate centimeters into miles.

Neal: "Seriously you must know "why" something is designed before accepting that it's designed? Double standard."

Reading comprehension FAIL. Try again. The "why" is not a requirement; that's why I specifically labeled it "icing on the cake."

Neal Tedford: "God wouldn't have done it this way. What's really eating you... The earth was not formed in 144 hours and therefore I'm not seeking Christ anymore? "

Where did that come from, how does it relate to the subject, and when have I ever indicated any of that? The imaginary conversations you have in your head are leaking out. Mop up.

Neal Tedford: "Evolutionists have no metric or standard for determining design. If something in life was designed, evolutionists have no way of determining it. "

Then please, by all means, explain to us how to determine design from the object itself. "Well, if the object can be modified, then it must have been designed," simply does not cut it.

Neal Tedford: "Everything is automatically the result of evolution."

Again, what bizarre imaginary conversation are you having, and with whom? Who has ever said that everything is automatically the result of evolution? Canyons aren't. Planets aren't. Glaciers aren't.

Neal Tedford: Who would win a contest in producing the most change in DNA in E Coli... Venter software design or Lenski's evolution?

Well, Venter's obviously. What the fudge difference does that make? I honestly don't see what connection you're making in your head. It's like saying "Who would win in excavating rock over a 24 hour period, erosion, or a stick of dynamite? Dynamite; ergo, design is a valid inference for the origin of the Grand Canyon?" I can't imagine that even you are that dumb. Surely there must be some other connection that you haven't yet been able to communicate.

It's just out of pure morbid curiosity that I want to know how you think Venter's experiments have any bearing on whether DNA was designed or not.

ba77: Do you have a demonstrated example of undirected processes generating 500 bits or above of novel functional information?

Yeah, it's been mentioned here a few times. Elizabeth had a nice simulation based on random mutations and selection that generated 500 bits of information. Here is a thread on her blog with a follow-up discussion: Creating CSI with NS.

So you have a intelligently designed algorithm to prove undirected biological evolution is possible? And this is suppose to impress me how???

The fact is:

"There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject."James Shapiro - Molecular Biologist

yet we find:

Cells Are Like Robust Computational Systems, - June 2009Excerpt: Gene regulatory networks in cell nuclei are similar to cloud computing networks, such as Google or Yahoo!, researchers report today in the online journal Molecular Systems Biology. The similarity is that each system keeps working despite the failure of individual components, whether they are master genes or computer processors. ,,,,"We now have reason to think of cells as robust computational devices, employing redundancy in the same way that enables large computing systems, such as Amazon, to keep operating despite the fact that servers routinely fail."http://www.sciencedaily.com/releases/2009/06/090616103205.htm

further notes:

In computer science we recognize the algorithmic principle described by Darwin - the linear accumulation of small changes through random variation - as hill climbing, more specifically random mutation hill climbing. However, we also recognize that hill climbing is the simplest possible form of optimization and is known to work well only on a limited class of problems.Watson R.A. - 2006 - Compositional Evolution - MIT Press - Pg. 272

Signature In The Cell - ReviewExcerpt: There is absolutely nothing surprising about the results of these (evolutionary) algorithms. The computer is programmed from the outset to converge on the solution. The programmer designed to do that. What would be surprising is if the program didn't converge on the solution. That would reflect badly on the skill of the programmer. Everything interesting in the output of the program came as a result of the programmer's skill-the information input. There are no mysterious outputs.Software Engineer - quoted to Stephen Meyerhttp://www.scribd.com/full/29346507?access_key=key-1ysrgwzxhb18zn6dtju0

You are wrong. It's an intelligently designed simulation of an unguided algorithm. We can intelligently simulate the trajectory of a planet. That does not mean the trajectory represents intelligent falling. :)

I realize that it would require a monumental paradigm shift for you from copying and pasting stuff that you don't understand to actually comprehending the details of a simulation, but it is well worth trying, assuming you have the stamina. Go ahead and try it.

Well oleg, perhaps you could actually get a 'simple' cell to pass the 500 bit UPB so as to actually prove the point you are claiming is already a proven fact??? Really! Do I have to program a computer to simulate gravity for you so as to prove to you that gravity actually works instead of just actually dropping a ball in front of you and showing you first hand?? Of course not! Why are you so willing to settle for anything less than an actual demonstration?? It simply is not even in the field of empirical science for you to play silly games like this!

Scant search for the MakerExcerpt: But where is the experimental evidence? None exists in the literature claiming that one species has been shown to evolve into another. Bacteria, the simplest form of independent life, are ideal for this kind of study, with generation times of 20 to 30 minutes, and populations achieved after 18 hours. But throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another, in spite of the fact that populations have been exposed to potent chemical and physical mutagens and that, uniquely, bacteria possess extrachromosomal, transmissible plasmids. Since there is no evidence for species changes between the simplest forms of unicellular life, it is not surprising that there is no evidence for evolution from prokaryotic to eukaryotic cells, let alone throughout the whole array of higher multicellular organisms. - Alan H. Linton - emeritus professor of bacteriology, University of Bristol.http://www.timeshighereducation.co.uk/story.asp?storycode=159282

The Law of Physicodynamic Insufficiency - Dr David L. Abel - November 2010Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”,,, After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.”http://www-qa.scitopics.com/The_Law_of_Physicodynamic_Insufficiency.html

You are moving the goalposts. You asked for "a demonstrated example of undirected processes generating 500 bits or above of novel functional information." I gave you that example. Now you don't like the fact that it is simulated. But that's beside the point. The process by which Liz's algorithm gets into its target space is unguided by a human. It relies on random mutations and on natural selection. It is proof of principle.

It cracks me up that you can't stay on message. You throw in for good measure a quote from the horse doctor (who hasn't a slightest clue about the information concepts he uses in his word salad). You mention antibiotic resistance, which has nothing whatsoever to do with Liz's simulation. To what end? So that people would get impressed by your mad literature citation skills? Well, I am a scientist and I am not impressed. :)

"You are moving the goalposts. You asked for "a demonstrated example of undirected processes generating 500 bits or above of novel functional information." I gave you that example. Now you don't like the fact that it is simulated."

So you don't actually have to empirically demonstrate anything anymore in science you can just use a intelligently designed computer program to prove whatever you claim to be true is true??? Wow you have just taken science to a whole new level. OKIE DOKIE let's see if I can catch the hang of this simulated proof via computer thing that you are trying to clue me in on. I claim that it is an undeniable fact that people can stop multiple bullets in mid-air! Here is my proof:

ba77, you can't appreciate the beauty of this counter example, and that's OK. Bill Dembski, on the other hand, spends lots of his time trying to debunk such programs. Casey Luskin explained that for his target audience. Try reading that.

Derrick,Dr. Venter just stated in New scientist that “All living cells that we know of on this planet are ‘DNA software’-driven biological machines comprised of hundreds of thousands of protein robots, coded for by the DNA, that carry out precise functions,” And“ The digital and biological worlds are becoming interchangeable,”http://www.newscientist.com/blogs/culturelab/2012/07/passing-the-baton-of-life---from-schrodinger-to-venter.html

Using your logic, the question then is “Well man can design software, does that mean all software are designed?”

If we were to poll the average college educated person on the street this question, we all know the overwhelming majority would answer YES! Why?Consider that the average college educated person on the street endowed with all of his education and intelligence does not have the slightest clue or know how to program software and has also observed throughout his life that all known software programs originate from a very smart mind! Can you then blame them for being skeptical when they are then being told that NO intelligent intervention was necessary to evolve “DNA software’-driven biological machines comprised of hundreds of thousands of protein robots, coded for by the DNA, that carry out precise functions”?

And can you blame them for considering the alternative, that perhaps an intelligent agent programmed this software?

Especially when you have eminent scientists like Paul Davies stating:“Instead, the living cell is best thought of as a supercomputer – an information processing and replicating system of astonishing complexity. DNA is not a special life-giving molecule, but a genetic databank that transmits its information using a mathematical code. Most of the workings of the cell are best described, not in terms of material stuff – hardware – but as information, or software. Trying to make life by mixing chemicals in a test tube is like soldering switches and wires in an attempt to produce Windows 98. It won’t work because it addresses the problem at the wrong conceptual level."

Lastly, can you then blame them for concluding that materialists are just soldering switches and wires?

Derrick - by "everything" I meant in my haste everything in biology in the history of life is automatically assumed to have evolved regardless if evolutionists know the specifics of how, why or when. Why? because you've got bird beaks and such to extrapolate.

Of course natural selection is not intentional (although the way evolutionists talk you would think so sometimes), but it does effect alleles. Evolutionists are asking us to place a lot of faith in their mechanisms for creating genes. What Venter and others show is the tremendous potential for design upon DNA. It's not only a good fit but an elegant fit. Of course we can't go back in history and know exactly how the creator did it, but what these scientists have shown is that intentional design is a reality for changing DNA quickly. It seems you agree, but have trouble believing that design can come from any being except humans. I think nearly everyone sees design in life, but because they can't see God, they don't believe. Some would rather place their faith in natural selection and believe that in the past it did a whole lot more than what we see it capable of actually doing.

It takes much more faith to believe in the power of your mechanisms than in design.

Sorry Bob, but you're still an idiot. When Venter talks about 'DNA software' IN QUOTES he's making an ANALOGY to human produced computer software. That still doesn't mean because humans produce computer software that DNA is designed.

Derrick - by "everything" I meant in my haste everything in biology in the history of life is automatically assumed to have evolved regardless if evolutionists know the specifics of how, why or when. Why? because you've got bird beaks and such to extrapolate.

Bob, why don't you go buy a Biology 101 textbook so you'll stop repeating the same stupid misunderstandings about the evidence for evolution? Would it make your fat head explode?

" Cells are the basic unit of life New species and inherited traits are the product of evolution Genes are the basic unit of heredity An organism regulates its internal environment to maintain a stable and constant condition Living organisms consume and transform energy."

As you can see, there is not much "Evolution" here.Biology isn't dependent on Evolution (unless one creates the illusion of dependence), and by Evolution I mean the claim that "New species are the product of Evolution" (ie: RM & NS). As for "inherited traits", that position is entirely acceptable within ID's framework.

In the sentence: "New species are the product of Evolution", evolution doesn't necessarily mean "RM & NS". Speciation will involve mutations, certainly, but not necessarily selection. If a population subdivides into two diverging lineages, all that may separate them is random drift.

However, adaptation will also tend to occur, as will conservative selection.

And all evolutionary theory is perfectly compatible with an Intelligent Designer. In fact there's nothing that isn't, which is why it is problematic as a theory.

That was the year Charles Darwin published On the Origin of Species so it's a salient event in the history of biology. Of course, he built on the thinking and work of others who had gone before him so you could argue that the theory has roots that run much deeper than that.

" Cells are the basic unit of lifeNew species and inherited traits are the product of evolutionGenes are the basic unit of heredityAn organism regulates its internal environment to maintain a stable and constant conditionLiving organisms consume and transform energy."

As you can see, there is not much "Evolution" here.

Really? What do you think it is that evolves other than living organisms made of cells and genes that are able to survive long enough to reproduce because they are able to regulate their internal environment to maintain a stable and constant condition? It is what evolution is about.

Biology isn't dependent on Evolution (unless one creates the illusion of dependence), and by Evolution I mean the claim that "New species are the product of Evolution" (ie: RM & NS). As for "inherited traits", that position is entirely acceptable within ID's framework.

Biology is the branch of science which studies life. Like all sciences, the purpose is not just to amass data but to create explanations of how and why that data is what it is.

In science, a good working theory is the most highly-prized product of research. A good theory does things like making sense of the data already gathered, revealing relationships in data that were not previously understood, pointing to new lines of research, predicting where previously unknown data can be found and so on.

In biology, evolution is the preeminent theory because, for the people actually working in the field, it does all of the above better than anything else. If ID could do the above better than evolution that is what scientists would be using. But it doesn't. It doesn't even come close.

As you can see, there is not much "Evolution" here.Biology isn't dependent on Evolution (unless one creates the illusion of dependence), and by Evolution I mean the claim that "New species are the product of Evolution" (ie: RM & NS).

from the very same Wiki article you cite:

"Foundations of modern biology

Much of modern biology can be encompassed within five unifying principles: cell theory, evolution, genetics, homeostasis, and energy

Evolution:

A central organizing concept in biology is that life changes and develops through evolution, and that all life-forms known have a common origin."

"Much of modern biology can be encompassed within five unifying principles: cell theory, evolution, genetics, homeostasis, and energy"

You have to define what you mean by Evolution. If you mean the unvalidated (and invalid) mechanism of Evolution of new species via NS & RM, then of course Biology by default does not (and should not) require it as a unification. Its nothing more than a hypothesis and anyone's expert opinion is up for grabs, including James Shapiro, John A. Davison etc....There is a difference between "I hypothesize that species x arisen by NS & RM" vs. what Evolutionists seem to be saying that "I am absolutely certain species x arisen by NS & RM". Is the latter correct Thorton? Do you hold this religious based position?

ThortonJuly 19, 2012 2:52 PMSorry Bob, but you're still an idiot. When Venter talks about 'DNA software' IN QUOTES he's making an ANALOGY to human produced computer software.

PG responds:I think you called him an idiot before you got your facts straight. Dr Venter is not stating DNA is "like" software, he is saying it "IS" software! Lets see what more Dr. Venter has to say about DNA software.

Article #1-Passing the baton of life - from Schrödinger to Venter“We are in what I call the digital age of biology,”

(Title of his Lecture)"All living cells that we know of on this planet are 'DNA software'-driven biological machines comprised of hundreds of thousands of protein robots, coded for by the DNA, that carry out precise functions,"

"We are now using computer software to design new DNA software."

“The digital and biological worlds are becoming interchangeable, he added, describing how scientists now simply send each other the information to make DIY biological material rather than sending the material itself. ”http://www.newscientist.com/blogs/culturelab/2012/07/passing-the-baton-of-life---from-schrodinger-to-venter.html

Article #2 -Digitizing biology: what is life now?Dr Venter went on to elaborate on the rapidly diminishing distinction between biological code and digital code, making the argument that...

“everything can be reduced to ones and zeros”.

"I describe DNA as the software and when we activate a synthetic genome in a cell we describe it as ‘booting up’, the same way you would boot up software on a computer."http://www.scienceomega.com/article/472/digitising-biology-what-is-life-now

Article #3 -Leading geneticist heralds digital age of biologyTHE LINE separating the digital world and the biological world is blurring and may soon fade away...

“We are in what I call the digital age of biology,”

He repeatedly returned to his theme of the interchangability of the digital and biological worlds...

“Life is a DNA software system,” he said. “If you change the software you change the species.”

“The DNA itself is an analogue code, in turn converted into digital codes that in turn delivered the proteins which make things happen in the cell.”

“I call the process digitizing biology,” he said. The DNA is the software of life, while the proteins are the hardware of life, mechanistic entities, natures robots.”http://www.irishtimes.com/newspaper/ireland/2012/0713/1224319967899.html

Article #4-Rewriting the software of life"DNA is really just software", says J Craig Venter, the world's most famous genetic scientist.The idea of the world’s most famous genetic scientist addressing a group of computer nerds, web designers and geeks of every stripe might have seemed incongruous two decades ago. But, as J Craig Venter puts it, "DNA is really just software, and few people know code better than this audience." http://mg.co.za/article/2011-03-16-rewriting-the-software-of-life/

Article #5 -TIME:Science fiction made fact. Venter: “The other thing you might have thought science-fiction, there's now little distinction between computer code and genetic code, and we readily convert one into another. So when we see what's a genome we're converting what we call the analogue DNA code into digital code. I've described that as digitizing biology."

"We are DNA software systems, [with] genetic code constantly driving new production of proteins. And proteins are simply robots that are chemically defined."http://www.time.com/time/health/article/0,8599,2119649,00.html#ixzz217v4aTeJ

So if Biology is going digital, then as Paul Davies asked " How did nature go digital?"Many of us are asking the same question...

Sorry C29, but Venter is still making an ANALOGY between human produced software and DNA. It's no different than if he said airplane wings and bird wings are both wings. Because the human produced one is designed doesn't make the naturally occurring analogous one be designed too.

I know the Olympics are almost here, but are you sure you want to be handed the stupidity torch from Tedford and run with it?

"In the sentence: "New species are the product of Evolution", evolution doesn't necessarily mean "RM & NS". Speciation will involve mutations, certainly, but not necessarily selection. If a population subdivides into two diverging lineages, all that may separate them is random drift."

computerist29, you may be interested in this quote in the latest article by Dr. Ann Gauger,

Dr. Ann Gauger: This is an interesting turn in evolutionary thinking. People have been saying for years, "Of course evolution isn't random, it's directed by natural selection. It's not chance, it's chance and necessity." But in recent years the rhetoric has changed. Now evolution is constrained. Not all options are open, and natural selection is not the major player, it's the happenstance of genetic drift that drives change. But somehow it all happens anyway, and evolution gets the credit.http://www.evolutionnews.org/2012/07/on_enzymes_and062391.html

computerist29, you may appreciate the implications of this following article that just came out:

Researchers produce first complete computer model of an organism - July 20, 2012Excerpt: In a breakthrough effort for computational biology, the world's first complete computer model of an organism has been completed, Stanford researchers reported in the journal Cell.,,,Most biological experiments, however, still take a reductionist approach to this vast array of data: knocking out a single gene and seeing what happens. "Many of the issues we're interested in aren't single-gene problems," said Covert. "They're the complex result of hundreds or thousands of genes interacting.",,,Mycoplasma genitalium is a humble parasitic bacterium, known mainly for showing up uninvited in human urogenital and respiratory tracts. But the pathogen also has the distinction of containing the smallest genome of any free-living organism – only 525 genes, as opposed to the 4,288 of E. coli, a more traditional laboratory bacterium.,,,Even at this small scale, the quantity of data that the Stanford researchers incorporated into the virtual cell's code was enormous. The final model made use of more than 1,900 experimentally determined parameters. To integrate these disparate data points into a unified machine, the researchers modeled individual biological processes as 28 separate "modules," each governed by its own algorithm. These modules then communicated to each other after every time step, making for a unified whole that closely matched M. genitalium's real-world behavior.http://phys.org/news/2012-07-researchers-produce-first-complete-computer.html

Reminds me of this comment from yesterday:

How we could create life: The key to existence will be found not in primordial sludge, but in the nanotechnology of the living cell - Paul Davies - 2002Excerpt: Instead, the living cell is best thought of as a supercomputer – an information processing and replicating system of astonishing complexity. DNA is not a special life-giving molecule, but a genetic databank that transmits its information using a mathematical code. Most of the workings of the cell are best described, not in terms of material stuff – hardware – but as information, or software. Trying to make life by mixing chemicals in a test tube is like soldering switches and wires in an attempt to produce Windows 98. It won’t work because it addresses the problem at the wrong conceptual level. - Paul Davieshttp://www.guardian.co.uk/education/2002/dec/11/highereducation.uk

"In the sentence: "New species are the product of Evolution", evolution doesn't necessarily mean "RM & NS". Speciation will involve mutations, certainly, but not necessarily selection. If a population subdivides into two diverging lineages, all that may separate them is random drift."

OK, will RM AND/OR NS suffice?

No. You also need to include the facdtors that induced the subdivision of the population.

Of course, I am not really sure what you mean by "new species". Are you talking about speciation events, or are you talking about change in population morphology down a single lineage?

Actually I find "RM+NS" a very poor description of Darwinian mechanisms anyway. The two ingredients are: a) novel heritable phenotypic variation where b) different variants have different probabilities of reproductive success.

An additional ingredient is required for speciation (but not for evolution, adaptive or otherwise, down one lineage, nor for conservation down a lineage) which is the separation of a sub-population from the rest of the population by some factor.

think the problem is one of context. Evolutionists will shift the context up or down as needed in order to "alleviate" the initial problem.

I am not sure what you mean by this. What I do see, repeatedly, is attempts by "evolutionists" to be precise about what evolutionary theory entails, only to be accused of "equivocating" when precisely the opposite is being attempted.

Here are some expressions which I frequently find equivocated, or, at best used misleadingly, by ID proponents:

ThortonJuly 20, 2012 6:16 AM>Sorry C29, but Venter is still making an ANALOGY between human produced software and DNA. It's no different than if he said airplane wings and bird wings are both wings. Because the human produced one is designed doesn't make the naturally occurring analogous one be designed too.”PG responds:Lets use your exact words and replace the word “wing” ..“It's no different than if he said Human software and DNA software are both software.” “Because the human produced one is designed doesn't make the naturally occurring analogous one be designed too.”Sure, its is true that just because DNA is software just like human software, it doesn’t prove it was designed. However, the fact is that Venter is ushering the age of “Digital biology” and the question that then needs to be answered is “How did nature go digital”?

Apparently, some posters here are continuing to object to Dr. Venter’s continued statements that Biology is Digital and DNA IS software, and in denial are claiming its all just an analogy. Lets review AGAIN if what Venter is saying about DNA is just an analogy…

"All living cells that we know of on this planet are 'DNA software'-driven biological machines comprised of hundreds of thousands of protein robots, coded for by the DNA, that carry out precise functions," said Venter. "We are now using computer software to design new DNA software."

Dr Venter went on to elaborate on the rapidly diminishing distinction between biological code and digital code, making the argument that...

“everything can be reduced to ones and zeros”.http://www.scienceomega.com/article/472/digitising-biology-what-is-life-now

"The idea of the world’s most famous genetic scientist addressing a group of computer nerds, web designers and geeks of every stripe might have seemed incongruous two decades ago. But, as J Craig Venter puts it, DNA is really just software—and few people know code better than this audience.”

“Having learned to “read” genetic code, they are learning how to “write” it.”

Their first breakthrough came when they proved in 2007 that they could take a single piece of DNA (a chromosome) from one species of bacteria and transplant it into another, and that the recipient bacteria would immediately began “reading” the software of the DNA. As Venter puts it “life is DNA software—you change the software, you change the species”.

“This proved challenging, particularly when a single mistaken letter could (and did) stop the whole process from working. “Just like software engineers have debuggers, we had to develop debugging technology,” says Venter somewhat ruefully.”

But, in May of 2010, after years of patient work they succeeded and the first ever artificial life, “whose parent”, as Venter is fond of saying, “is a computer”http://mg.co.za/article/2011-03-16-rewriting-the-software-of-life/

Apparently, some posters here are continuing to object to Dr. Venter’s continued statements that Biology is Digital and DNA IS software, and in denial are claiming its all just an analogy.

[...]

“everything can be reduced to ones and zeros”.http://www.scienceomega.com/article/472/digitising-biology-what-is-life-now

The binary code used by computers is a versatile language that is valuable precisely because it can be used by computers. But anyone who thinks life is all digital should ask themselves how many people, including computer nerds and geeks, actually think and talk in binary.

The fact is, binary code is, in a sense, a language like the on I'm using now. Languages are valuable because they enable us to create, manipulate and communicate models of the world around us. The key distinction to remember, however, is that the language is not the same as the thing being described, the model is not the same as the thing being modeled. In a broad sense they are all analogies.

There are two other aspects of Venter's work to consider.

First, he is exploiting what has been discovered about the genome and how changes to it, whether artificially induced or naturally occuring, can effect the organism. That is, in effect, a validation of evolutionary theory. His work would not happen if the theory was wrong.

Second, his work suggests that living things are nothing more than biological machines whose design can be manipulated by anyone with the right knowledge and tools. That is unlikely to set well with the religious beliefs of most ID proponents and certain not to set well with the beliefs of out-and-out creationists.

“This proved challenging, particularly when a single mistaken letter could (and did) stop the whole process from working. “Just like software engineers have debuggers, we had to develop debugging technology,” says Venter somewhat ruefully.”

You go on to say:

"First, he is exploiting what has been discovered about the genome and how changes to it, whether artificially induced or naturally occuring, can effect the organism. That is, in effect, a validation of evolutionary theory. His work would not happen if the theory was wrong."

Do you find anything wrong with this reasoning? If you follow and understand ID, you know the answer to this. Hint: emphasis on the bold

This is an over-blown claim. Venter has not and cannot design DNA sequences de novo that function in line with prediction. Sure, people can (though, I am not sure to what extent it has been done, other than using and adapting existing sequences) synthesize and splice sequences, then test them to see what results ensue, but this is not "design", it is a form of random mutation follwed by selection. The same process that has produces the diversity of life we see on Earth.

What is certainly true is that we are now using computer-implemented evolutionary algorithms to design all kinds of things, because it is often more effective at solving real problems than we intelligent designers are.

In computer science we recognize the algorithmic principle described by Darwin - the linear accumulation of small changes through random variation - as hill climbing, more specifically random mutation hill climbing. However, we also recognize that hill climbing is the simplest possible form of optimization and is known to work well only on a limited class of problems.Watson R.A. - 2006 - Compositional Evolution - MIT Press - Pg. 272

Applied Darwinism: A New Paper from Bob Marks and His Team, in BIO-Complexity - Doug Axe 2012Excerpt: Furthermore, if you dig a bit beyond these papers and look at what kinds of problems this technique (Steiner Tree) is being used for in the engineering world, you quickly find that it is of extremely limited applicability. It works for tasks that are easily accomplished in a huge number of specific ways, but where someone would have to do a lot of mindless fiddling to decide which of these ways is best.,, That's helpful in the sense that we commonly find computers helpful -- they do what we tell them to do very efficiently, without complaining. But in biology we see something altogether different. We see elegant solutions to millions of engineering problems that human ingenuity cannot even begin to solve.http://www.evolutionnews.org/2012/04/applied_darwini058591.html

Signature In The Cell - ReviewExcerpt: There is absolutely nothing surprising about the results of these (evolutionary) algorithms. The computer is programmed from the outset to converge on the solution. The programmer designed to do that. What would be surprising is if the program didn't converge on the solution. That would reflect badly on the skill of the programmer. Everything interesting in the output of the program came as a result of the programmer's skill-the information input. There are no mysterious outputs.Software Engineer - quoted to Stephen Meyerhttp://www.scribd.com/full/29346507?access_key=key-1ysrgwzxhb18zn6dtju0

A Darwinian Enigma: Defending The Preposterous After Having Been InformedExcerpt: I’m thoroughly familiar with Monte Carlo methods. Trial and error can be a useful tool in an intelligently designed computer program, given a limited search space, sufficient computational resources, and a goal in mind.None of this has anything to do with extrapolating Monte Carlo methods in computation to the origin of information in biological systems.Unsupported extrapolations such as this are the hallmark of Darwinian speculation, which is the antithesis of rigorous scientific investigation. -Gil Dodgen - Programmer of 'Perfect Play Checkers'

Algorithmic Information Theory, Free Will and the Turing Test - Douglas S. RobertsonExcerpt: Chaitin’s Algorithmic Information Theory shows that information is conserved under formal mathematical operations and, equivalently, under computer operations. This conservation law puts a new perspective on many familiar problems related to artificial intelligence. For example, the famous “Turing test” for artificial intelligence could be defeated by simply asking for a new axiom in mathematics. Human mathematicians are able to create axioms, but a computer program cannot do this without violating information conservation. Creating new axioms and free will are shown to be different aspects of the same phenomena: the creation of new information.http://cires.colorado.edu/~doug/philosophy/info7.pdf

Here is what George Chaitin, a world-famous mathematician and computer scientist, said about the limits of his computer program trying to prove evolution was mathematically feasible:

At last, a Darwinist mathematician tells the truth about evolution - VJT - November 2011Excerpt: In Chaitin’s own words, “You’re allowed to ask God or someone to give you the answer to some question where you can’t compute the answer, and the oracle will immediately give you the answer, and you go on ahead.”http://www.uncommondescent.com/intelligent-design/at-last-a-darwinist-mathematician-tells-the-truth-about-evolution/

Here is the video where, at the 30:00 minute mark, you can hear the preceding quote from Chaitin's own mouth in full context:

Life as Evolving Software, Greg Chaitin at PPGC UFRGShttp://www.youtube.com/watch?v=RlYS_GiAnK8

Moreover, at the 40:00 minute mark of the video Chaitin readily admits that Intelligent Design is the best possible way to get evolution to take place, and at the 43:30 minute mark Chaitin even tells of a friend pointing out that the idea Evolutionary computer model that Chaitin has devised does not have enough time to work. And Chaitin even agreed that his friend had a point, although Chaitin still ends up just 'wanting', and not ever proving, his idea Darwinian mathematical model to be true!

bornagain77 (quoting): "In computer science we recognize the algorithmic principle described by Darwin - the linear accumulation of small changes through random variation - as hill climbing, more specifically random mutation hill climbing. However, we also recognize that hill climbing is the simplest possible form of optimization and is known to work well only on a limited class of problems." Watson R.A. - 2006 - Compositional Evolution - MIT Press - Pg. 272

You really need to quit quote-mining people. Someone might think you were dishonest rather than simply ignorant. Of course, ignorance is curable, and you would have detected your error if you had enough intellectual curiosity to have actually read Watson's book. You didn't even use the complete title.

"No biological concept has had greater impact on the way we view ourselves and the world around us than the theory of evolution by natural selection. Darwin's masterful contribution was to provide an algorithmic model (a formal step-by-step procedure) of how adaptation may take place in biological systems. However, the simple process of linear incremental improvement that he described is only one algorithmic possibility, and certain biological phenomena provide the possibility of implementing alternative processes. In Compositional Evolution, Richard Watson uses the tools of computer science and computational biology to show that certain mechanisms of genetic variation (such as sex, gene transfer, and symbiosis) allowing the combination of preadapted genetic material enable an evolutionary process, compositional evolution, that is algorithmically distinct from the Darwinian gradualist framework."

bornagain77: So do you agree with Watson that neo-Darwinism, as a 'gradual' process, is not feasible to explain life?

Couple of points: Sexual recombination has been a part of Neodarwinian Theory since its inception; Today's Theory of Evolution is not the same as your father's Theory of Evolution; Watson is a mathematician studying evolutionary processes, modeling evolution via stochastic processes.

bornagain77: So do you agree with Watson that neo-Darwinism, as a 'gradual' process, is not feasible to explain life?

Try not to confuse a model with the thing itself. Darwin proposed an incremental process of adaptation, which explained much of the history of macroscopic evolutionary adaptations. He had no mathematical model other than bifurcating descent, but it would be akin to simple evolutionary hill-climbing. Later, this theory was combined with particulate and population genetics to provide the so-called Modern Synthesis, which is nearly a century old and superseded by generations of research.

Modern complex network theory implies that evolution occurs by many small changes, occasional large changes, and the rare revolution. Also, when you include various sorts of recombination, that implies the ability to swap modularly. This understanding of complex iterative processes only came with better modeling, especially by computer.

bornagain77: If so have you adopted Shapiro's 'natural genetic engineering' as a more feasible alternative?

Natural Genetic Engineering is a bit different, but still consistent with evolutionary processes. Organisms have a memory of past evolution. In simple models, these structures decay. But in an environment that might oscillate between two or more poles, it is quite possible for the phenotype to be able to likewise oscillate. Or, even more interesting, there could be a standard toolkit, whereby various modules can be swapped in an out, depending on the environmental situation. They don't decay because they are always being used for some function or other. Some of this may occur epigenetically, and some of it may occur genetically. There's still a lot unknown about the specifics, but all of these are consistent with what we know of evolutionary networks, that is, stochastic processes under selection.

‘Now one more problem as far as the generation of information. It turns out that you don’t only need information to build genes and proteins, it turns out to build Body-Plans you need higher levels of information; Higher order assembly instructions. DNA codes for the building of proteins, but proteins must be arranged into distinctive circuitry to form distinctive cell types. Cell types have to be arranged into tissues. Tissues have to be arranged into organs. Organs and tissues must be specifically arranged to generate whole new Body-Plans, distinctive arrangements of those body parts. We now know that DNA alone is not responsible for those higher orders of organization. DNA codes for proteins, but by itself it does insure that proteins, cell types, tissues, organs, will all be arranged in the body. And what that means is that the Body-Plan morphogenesis, as it is called, depends upon information that is not encoded on DNA. Which means you can mutate DNA indefinitely. 80 million years, 100 million years, til the cows come home. It doesn’t matter, because in the best case you are just going to find a new protein some place out there in that vast combinatorial sequence space. You are not, by mutating DNA alone, going to generate higher order structures that are necessary to building a body plan. So what we can conclude from that is that the neo-Darwinian mechanism is grossly inadequate to explain the origin of information necessary to build new genes and proteins, and it is also grossly inadequate to explain the origination of novel biological form.’ - Stephen Meyer - (excerpt taken from Meyer/Sternberg vs. Shermer/Prothero debate - 2009)

Epigenetics and the "Piano" Metaphor - January 2012 Excerpt: And this is only the construction of proteins we're talking about. It leaves out of the picture entirely the higher-level components -- tissues, organs, the whole body plan that draws all the lower-level stuff together into a coherent, functioning form. What we should really be talking about is not a lone piano but a vast orchestra under the directing guidance of an unknown conductor fulfilling an artistic vision, organizing and transcending the music of the assembly of individual players. http://www.evolutionnews.org/2012/01/epigenetics_and054731.html

Perhaps you care to provide empirical evidence that Darwinian processes can arrive at even a single novel functional protein domain? Or am I suppose to take your word that it can happen?

No, you are supposed to consider the evidence. There is sufficient evidence for the existence of evolutionary processes to make it possible that "novel functional protein domain[s]" can arise from them. There is certainly more evidence for evolutionary process than there is for some alien Intelligent Designer or for the Christian God.

The fact that we have not observed such a thing yet does not mean that it cannot happen. It is like criticizing evolution because no one has seen a new species of large animal emerge. But human beings have only been practising modern science for a few hundred years at best. The whole of recorded human history only goes back maybe 10,000 years. We haven't been around long enough and we certainly haven't being paying attention for long enough to observe events which could take several million years. So the fact we haven't directly observed something like that proves nothing

What you have to do is look for the sort of clues you would expect to see if such event were happening or had happened. That is what science is looking for and has found.

What are the alternatives - an alien Intelligent Designer or a God? You have no credible evidence that such beings exist and certainly no detailed explanation of how they might have done what you claim they did.

Okie Dokie you are claiming 'unseen' random processes can create 'observable' functional protein domains, whereas IDists claim unseen intelligence is necessary to explain the existence of functional protein domains (as well as the existence of the laws of physics, the existence of the mass-energy within those laws of physics, as well as the big bang itself.) so Where's your evidence that 'unseen' random processes can generate 'observable' novel functional protein domains? You simply have no empirical evidence for your claim!

I've even got the ideal experiment for you to try prove your point:

Blackholes- The neo-Darwinists ultimate ‘god of randomness’ which can create all life in the universe (according to them)https://docs.google.com/document/d/1fxhJEGNeEQ_sn4ngQWmeBt1YuyOs8AQcUrzBRo7wISw/edit?hl=en_US

Creating Life in the Lab: How New Discoveries in Synthetic Biology Make a Case for the Creator - Fazale RanaExcerpt of Review: ‘Another interesting section of Creating Life in the Lab is one on artificial enzymes. Biological enzymes catalyze chemical reactions, often increasing the spontaneous reaction rate by a billion times or more. Scientists have set out to produce artificial enzymes that catalyze chemical reactions not used in biological organisms. Comparing the structure of biological enzymes, scientists used super-computers to calculate the sequences of amino acids in their enzymes that might catalyze the reaction they were interested in. After testing dozens of candidates,, the best ones were chosen and subjected to “in vitro evolution,” which increased the reaction rate up to 200-fold. Despite all this “intelligent design,” the artificial enzymes were 10,000 to 1,000,000,000 times less efficient than their biological counterparts. Dr. Rana asks the question, “is it reasonable to think that undirected evolutionary processes routinely accomplished this task?”http://www.amazon.com/gp/product/0801072093

Here is my proof that intelligence can build a protein binding site:

Viral-Binding Protein Design Makes the Case for Intelligent Design Sick! (as in cool) - Fazale Rana - June 2011Excerpt: When considering this study, it is remarkable to note how much effort it took to design a protein that binds to a specific location on the hemagglutinin molecule. As biochemists Bryan Der and Brian Kuhlman point out while commenting on this work, the design of these proteins required:"...cutting-edge software developed by ~20 groups worldwide and 100,000 hours of highly parallel computing time. It also involved using a technique known as yeast display to screen candidate proteins and select those with high binding affinities, as well as x-ray crystallography to validate designs.2"If it takes this much work and intellectual input to create a single protein from scratch, is it really reasonable to think that undirected evolutionary processes could accomplish this task routinely?In other words, the researchers from the University of Washington and The Scripps Institute have unwittingly provided empirical evidence that the high-precision interactions required for PPIs requires intelligent agency to arise. Sick!http://www.reasons.org/viral-binding-protein-design-makes-case-intelligent-design-sick-cool

2.capable of operating or functioning: When will the ventilating system be functional again?3.having or serving a utilitarian purpose; capable of serving the purpose for which it was designed: functional architecture; a chair that is functional as well as decorative. http://dictionary.reference.com/browse/functional

‘Now one more problem as far as the generation of information. It turns out that you don’t only need information to build genes and proteins, it turns out to build Body-Plans you need higher levels of information; Higher order assembly instructions. DNA codes for the building of proteins, but proteins must be arranged into distinctive circuitry to form distinctive cell types. Cell types have to be arranged into tissues. Tissues have to be arranged into organs. Organs and tissues must be specifically arranged to generate whole new Body-Plans, distinctive arrangements of those body parts. We now know that DNA alone is not responsible for those higher orders of organization. DNA codes for proteins, but by itself it does insure that proteins, cell types, tissues, organs, will all be arranged in the body. And what that means is that the Body-Plan morphogenesis, as it is called, depends upon information that is not encoded on DNA. Which means you can mutate DNA indefinitely. 80 million years, 100 million years, til the cows come home. It doesn’t matter, because in the best case you are just going to find a new protein some place out there in that vast combinatorial sequence space. You are not, by mutating DNA alone, going to generate higher order structures that are necessary to building a body plan. So what we can conclude from that is that the neo-Darwinian mechanism is grossly inadequate to explain the origin of information necessary to build new genes and proteins, and it is also grossly inadequate to explain the origination of novel biological form.’ - Stephen Meyer - (excerpt taken from Meyer/Sternberg vs. Shermer/Prothero debate - 2009)

So an amino acid sequence that is designed to fold into the specified and complex shape required to bind to a specific molecule would be functional. Is that correct?

Functional in not only in folding and binding but also in serving a utilitarian purpose:

as to the reference you were probably were going to cite:

A Man-Made ATP-Binding Protein Evolved Independent of Nature Causes Abnormal Growth in Bacterial CellsExcerpt: "Recent advances in de novo protein evolution have made it possible to create synthetic proteins from unbiased libraries that fold into stable tertiary structures with predefined functions. However, it is not known whether such proteins will be functional when expressed inside living cells or how a host organism would respond to an encounter with a non-biological protein. Here, we examine the physiology and morphology of Escherichia coli cells engineered to express a synthetic ATP-binding protein evolved entirely from non-biological origins. We show that this man-made protein disrupts the normal energetic balance of the cell by altering the levels of intracellular ATP. This disruption cascades into a series of events that ultimately limit reproductive competency by inhibiting cell division."http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0007385

Protein Life Times: Just-Right Evidence for Design - Fazale Rana PhD. biochemistryExcerpt: Researchers learned that the amino acid sequences are exquisitely arranged to precisely balance the need for structural stability, while minimizing aggregation propensity.,,, Yet the optimization of proteins is not limited to their aggregation propensities. A cascade of optimization characterizes protein structure and function. In The Cell’s Design, I described a number of other ways that protein structure is optimized.http://www.reasons.org/articles/protein-life-times-just-right-evidence-for-design

bornagain77: It turns out that you don’t only need information to build genes and proteins, it turns out to build Body-Plans you need higher levels of information; Higher order assembly instructions.

Meyer waves his hands a lot and makes a lot of unsupported claims. That's why videos are not the best resource.

bornagain77: Perhaps you care to provide empirical evidence that Darwinian processes can arrive at even a single novel functional protein domain? Or am I suppose to take your word that it can happen?

bornagain77: Functional in not only in folding and binding but also in serving a utilitarian purpose:

So really you don't mean a functional protein as most scientists understand the term, but one that is integrated within the living cell. As most protein domains evolved long ago, asking for an observation of such evolution is like asking why we don't observe reptiles evolving into birds or fish into frogs.

Instead, you have to consider the historical evidence, such as the nested hierarchy and the fossil succession, which most scientists consider to be conclusive support for evolution.